Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, PO Box 65, 8200 AB Lelystad, the Netherlands.
J Dairy Sci. 2011 Aug;94(8):4164-73. doi: 10.3168/jds.2010-4112.
Marker-assisted breeding value estimation is expected to increase the accuracy of estimated breeding values, especially for traits with low heritability. Several quantitative trait loci (QTL) have been found for somatic cell score and clinical mastitis. The objective of this study was to demonstrate marker-assisted breeding value estimation, combining data of genotyped and ungenotyped animals in a large pedigree population using either identical-by-descent (IBD) or identical-by-state (IBS) haplotypes for some previously identified QTL regions for somatic cell score and clinical mastitis in Finnish Ayrshire cattle. For both methods, QTL variances were estimated based on daughter yield deviations of genotyped bulls. The QTL explained only a small proportion of genetic variance, especially with IBS haplotypes. Using IBD haplotypes gave more reranking of bulls and cows than using IBS haplotypes. Cross-validation showed no increase in predictive ability when using IBS haplotypes compared with conventional breeding value estimation, whereas a decrease in predictive ability was observed with IBD haplotypes. Furthermore, computing time was lower and convergence was better with IBS haplotypes than with IBD haplotypes. In this study on mastitis resistance in Finnish Ayrshire, conventional breeding value estimation would be advocated because of the lack in improvement of accuracy and predictive ability when using marker-assisted breeding value estimation. However, in situations where IBS haplotypes would explain 10 to 20% or more of the genetic variance, marker-assisted breeding value estimation with IBS haplotypes may yield greater accuracy and predictive ability than conventional breeding value estimation.
标记辅助育种值估计有望提高估计育种值的准确性，特别是对于遗传力较低的性状。已经发现了几个与体细胞评分和临床乳腺炎相关的数量性状位点（QTL）。本研究的目的是展示标记辅助育种值估计，在一个大型 pedigree 群体中，结合已基因型和未基因型动物的数据，使用相同的被基因确定的（IBD）或相同的状态（IBS）单体型，来估计先前在芬兰 Ayrshire 牛中鉴定的体细胞评分和临床乳腺炎 QTL 区域的一些 QTL 方差。对于这两种方法，都是基于已基因型公牛的女儿产量偏差来估计 QTL 方差。QTL 只解释了遗传方差的一小部分，尤其是 IBS 单体型。与 IBS 单体型相比，使用 IBD 单体型可以更多地重新排列公牛和母牛。交叉验证显示，与传统育种值估计相比，使用 IBS 单体型并不能提高预测能力，而使用 IBD 单体型则观察到预测能力下降。此外，与 IBD 单体型相比，使用 IBS 单体型时计算时间更低，收敛性更好。在这项关于芬兰 Ayrshire 乳腺炎抗性的研究中，由于使用标记辅助育种值估计时准确性和预测能力没有提高，因此建议使用传统的育种值估计。然而，在 IBS 单体型解释 10%到 20%或更多遗传方差的情况下，使用 IBS 单体型的标记辅助育种值估计可能比传统的育种值估计具有更高的准确性和预测能力。
